Re: [galaxy-dev] latest galaxy-central version
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired. Are there any javascript errors? Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
It keeps doing posts, and I'm not seeing any new errors. POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in) Galaxy.currUser is undefined on Line 631 in history-panel.js When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things. -Robert On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
Hello, I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation. --Marten On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
It keeps doing posts, and I'm not seeing any new errors.
POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in)
Galaxy.currUser is undefined on Line 631 in history-panel.js
When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things.
-Robert
On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
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I updated to the stable release and reproduced the issue. Step to reproduce 1. go to admin 2. Manage data libraries 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start Screen shows strange formatting and "Job is running" for Bam file. python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat If I do a firefox refresh and go back to the library, the formatting is normal. I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert On Nov 4, 2013, at 12:45 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello,
I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: It keeps doing posts, and I'm not seeing any new errors.
POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms
When I did a browser refresh, I got the following javascript error: (I am logged in)
Galaxy.currUser is undefined on Line 631 in history-panel.js
When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things.
-Robert
On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello, Robert I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0. Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above? I'll investigate further. On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
I updated to the stable release and reproduced the issue.
Step to reproduce 1. go to admin 2. Manage data libraries<http://su2c-dev.ucsc.edu:8383/library_admin/browse_libraries> 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start
Screen shows strange formatting and "Job is running" for Bam file.
python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat
If I do a firefox refresh and go back to the library, the formatting is normal.
I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert
On Nov 4, 2013, at 12:45 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello,
I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
It keeps doing posts, and I'm not seeing any new errors.
POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in)
Galaxy.currUser is undefined on Line 631 in history-panel.js
When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things.
-Robert
On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Carl, Just to make sure I just deleted my tree and did a fresh checkout and tried a third time. It happened all three times. I'm using a postgres database and this time I started with a fresh config files and just changed the setting below. I didn't see the javascript error in Chrome, perhaps it is some strangeness in Firebug. I've seen strange errors before in Firebug. Attached are two screen grab of the lastest try before and after browser refresh. changeset: 11227:151b7d3b2f1b branch: stable tag: tip parent: 11219:5c789ab4144a user: Carl Eberhard <carlfeberhard@gmail.com> date: Tue Nov 05 11:33:06 2013 -0500 summary: History panel: fix naming bug in purge async error handling -Robert 29c29 < port = 8585 ---
#port = 8080 34c34 < host = 0.0.0.0
#host = 127.0.0.1 96d95 < database_connection = postgresql://localhost/medbookgalaxycentral3 542c541 < allow_library_path_paste = True
#allow_library_path_paste = False 599c598 < admin_users = baertsch@soe.ucsc.edu
#admin_users = None
On Nov 5, 2013, at 8:21 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Robert
I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0.
Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above?
I'll investigate further.
On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: I updated to the stable release and reproduced the issue.
Step to reproduce 1. go to admin 2. Manage data libraries 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start
Screen shows strange formatting and "Job is running" for Bam file.
python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat
If I do a firefox refresh and go back to the library, the formatting is normal.
I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert
On Nov 4, 2013, at 12:45 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello,
I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: It keeps doing posts, and I'm not seeing any new errors.
POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms
When I did a browser refresh, I got the following javascript error: (I am logged in)
Galaxy.currUser is undefined on Line 631 in history-panel.js
When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things.
-Robert
On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Thanks for the thorough report, Robert. I've added some sanity checking to the panel in default:11240:c271cdb443c6 My only guess as to why the panel javascript is trying to load at all in the library section is a link to the controller/datasets methods (unhide, delete, etc.) that still assume histories are in their own frames. Still investigating. On Tue, Nov 5, 2013 at 12:06 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
Carl, Just to make sure I just deleted my tree and did a fresh checkout and tried a third time. It happened all three times. I'm using a postgres database and this time I started with a fresh config files and just changed the setting below.
I didn't see the javascript error in Chrome, perhaps it is some strangeness in Firebug. I've seen strange errors before in Firebug.
Attached are two screen grab of the lastest try before and after browser refresh.
changeset: 11227:151b7d3b2f1b branch: stable tag: tip parent: 11219:5c789ab4144a user: Carl Eberhard <carlfeberhard@gmail.com> date: Tue Nov 05 11:33:06 2013 -0500 summary: History panel: fix naming bug in purge async error handling
-Robert
29c29 < port = 8585 ---
#port = 8080 34c34 < host = 0.0.0.0
#host = 127.0.0.1 96d95 < database_connection = postgresql://localhost/medbookgalaxycentral3 542c541 < allow_library_path_paste = True
#allow_library_path_paste = False 599c598 < admin_users = baertsch@soe.ucsc.edu
#admin_users = None
On Nov 5, 2013, at 8:21 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Robert
I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0.
Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above?
I'll investigate further.
On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
I updated to the stable release and reproduced the issue.
Step to reproduce 1. go to admin 2. Manage data libraries<http://su2c-dev.ucsc.edu:8383/library_admin/browse_libraries> 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start
Screen shows strange formatting and "Job is running" for Bam file.
python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat
If I do a firefox refresh and go back to the library, the formatting is normal.
I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert
On Nov 4, 2013, at 12:45 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello,
I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
It keeps doing posts, and I'm not seeing any new errors.
POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in)
Galaxy.currUser is undefined on Line 631 in history-panel.js
When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things.
-Robert
On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Carl, Thanks for building a great tool. Can you fix the library performance problem? Steps to reproduce: 1. http://su2c-dev.ucsc.edu/library 2. open library TCGA Pancan. It takes more than 20 seconds! -Robert On Nov 5, 2013, at 1:29 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Thanks for the thorough report, Robert.
I've added some sanity checking to the panel in default:11240:c271cdb443c6
My only guess as to why the panel javascript is trying to load at all in the library section is a link to the controller/datasets methods (unhide, delete, etc.) that still assume histories are in their own frames. Still investigating.
On Tue, Nov 5, 2013 at 12:06 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: Carl, Just to make sure I just deleted my tree and did a fresh checkout and tried a third time. It happened all three times. I'm using a postgres database and this time I started with a fresh config files and just changed the setting below.
I didn't see the javascript error in Chrome, perhaps it is some strangeness in Firebug. I've seen strange errors before in Firebug.
Attached are two screen grab of the lastest try before and after browser refresh.
changeset: 11227:151b7d3b2f1b branch: stable tag: tip parent: 11219:5c789ab4144a user: Carl Eberhard <carlfeberhard@gmail.com> date: Tue Nov 05 11:33:06 2013 -0500 summary: History panel: fix naming bug in purge async error handling
-Robert
29c29 < port = 8585 ---
#port = 8080 34c34 < host = 0.0.0.0
#host = 127.0.0.1 96d95 < database_connection = postgresql://localhost/medbookgalaxycentral3 542c541 < allow_library_path_paste = True
#allow_library_path_paste = False 599c598 < admin_users = baertsch@soe.ucsc.edu
#admin_users = None
<Screen Shot 2013-11-05 at 8.35.09 AM.png> <Screen Shot 2013-11-05 at 8.37.04 AM.png>
On Nov 5, 2013, at 8:21 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Robert
I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0.
Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above?
I'll investigate further.
On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: I updated to the stable release and reproduced the issue.
Step to reproduce 1. go to admin 2. Manage data libraries 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start
Screen shows strange formatting and "Job is running" for Bam file.
python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat
If I do a firefox refresh and go back to the library, the formatting is normal.
I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert
On Nov 4, 2013, at 12:45 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello,
I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: It keeps doing posts, and I'm not seeing any new errors.
POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms
When I did a browser refresh, I got the following javascript error: (I am logged in)
Galaxy.currUser is undefined on Line 631 in history-panel.js
When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things.
-Robert
On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
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Hi Robert, We are currently working on improving data libraries including the speed enhancements. In the meantime one of our users also reported that he is using for the dataset folders multiple libraries - each having less folder-depth which for him improves performance significantly. Maybe it will be of use to you. --Martin On Tue, Nov 5, 2013 at 5:19 PM, Robert Baertsch <robert.baertsch@gmail.com>wrote:
Carl, Thanks for building a great tool.
Can you fix the library performance problem?
Steps to reproduce: 1. http://su2c-dev.ucsc.edu/library 2. open library TCGA Pancan.
It takes more than 20 seconds! -Robert
On Nov 5, 2013, at 1:29 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Thanks for the thorough report, Robert.
I've added some sanity checking to the panel in default:11240:c271cdb443c6
My only guess as to why the panel javascript is trying to load at all in the library section is a link to the controller/datasets methods (unhide, delete, etc.) that still assume histories are in their own frames. Still investigating.
On Tue, Nov 5, 2013 at 12:06 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
Carl, Just to make sure I just deleted my tree and did a fresh checkout and tried a third time. It happened all three times. I'm using a postgres database and this time I started with a fresh config files and just changed the setting below.
I didn't see the javascript error in Chrome, perhaps it is some strangeness in Firebug. I've seen strange errors before in Firebug.
Attached are two screen grab of the lastest try before and after browser refresh.
changeset: 11227:151b7d3b2f1b branch: stable tag: tip parent: 11219:5c789ab4144a user: Carl Eberhard <carlfeberhard@gmail.com> date: Tue Nov 05 11:33:06 2013 -0500 summary: History panel: fix naming bug in purge async error handling
-Robert
29c29 < port = 8585 ---
#port = 8080 34c34 < host = 0.0.0.0
#host = 127.0.0.1 96d95 < database_connection = postgresql://localhost/medbookgalaxycentral3 542c541 < allow_library_path_paste = True
#allow_library_path_paste = False 599c598 < admin_users = baertsch@soe.ucsc.edu
#admin_users = None
<Screen Shot 2013-11-05 at 8.35.09 AM.png> <Screen Shot 2013-11-05 at 8.37.04 AM.png>
On Nov 5, 2013, at 8:21 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Robert
I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0.
Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above?
I'll investigate further.
On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
I updated to the stable release and reproduced the issue.
Step to reproduce 1. go to admin 2. Manage data libraries<http://su2c-dev.ucsc.edu:8383/library_admin/browse_libraries> 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start
Screen shows strange formatting and "Job is running" for Bam file.
python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat
If I do a firefox refresh and go back to the library, the formatting is normal.
I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert
On Nov 4, 2013, at 12:45 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hello,
I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
It keeps doing posts, and I'm not seeing any new errors.
POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in)
Galaxy.currUser is undefined on Line 631 in history-panel.js
When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things.
-Robert
On Nov 4, 2013, at 11:14 AM, James Taylor <james@jamestaylor.org> wrote:
Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired.
Are there any javascript errors?
Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console.
-- James Taylor, Associate Professor, Biology/CS, Emory University
On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update.
I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server.
During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted
Do you finish rendering the screen after the copy operation is complete?
-Robert
<Screen Shot 2013-11-04 at 10.53.02 AM.png>
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participants (5)
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Robert Baertsch